Human Gene SPTBN4 (ENST00000598249.6_5) from GENCODE V47lift37
  Description: spectrin beta, non-erythrocytic 4, transcript variant sigma1 (from RefSeq NM_020971.3)
Gencode Transcript: ENST00000598249.6_5
Gencode Gene: ENSG00000160460.17_11
Transcript (Including UTRs)
   Position: hg19 chr19:40,972,908-41,082,370 Size: 109,463 Total Exon Count: 36 Strand: +
Coding Region
   Position: hg19 chr19:40,978,529-41,081,475 Size: 102,947 Coding Exon Count: 35 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:40,972,908-41,082,370)mRNA (may differ from genome)Protein (2564 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
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MalacardsMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SPTN4_HUMAN
DESCRIPTION: RecName: Full=Spectrin beta chain, non-erythrocytic 4; AltName: Full=Beta-IV spectrin; AltName: Full=Spectrin, non-erythroid beta chain 3;
INTERACTION: Q9NRI5:DISC1; NbExp=3; IntAct=EBI-308543, EBI-529989;
SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton (By similarity). Cytoplasm, cell cortex (By similarity).
TISSUE SPECIFICITY: Abundantly expressed in brain and pancreatic islets.
SIMILARITY: Belongs to the spectrin family.
SIMILARITY: Contains 2 CH (calponin-homology) domains.
SIMILARITY: Contains 1 PH domain.
SIMILARITY: Contains 18 spectrin repeats.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: SPTBN4
Diseases sorted by gene-association score: myopathy, congenital, with neuropathy and deafness* (950)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 35.80 RPKM in Brain - Cerebellum
Total median expression: 201.15 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -197.10320-0.616 Picture PostScript Text
3' UTR -411.50895-0.460 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001589 - Actinin_actin-bd_CS
IPR001715 - CH-domain
IPR001605 - PH_dom-spectrin-type
IPR011993 - PH_like_dom
IPR001849 - Pleckstrin_homology
IPR018159 - Spectrin/alpha-actinin
IPR016343 - Spectrin_bsu
IPR002017 - Spectrin_repeat

Pfam Domains:
PF00169 - PH domain
PF00307 - Calponin homology (CH) domain
PF00435 - Spectrin repeat
PF11971 - CAMSAP CH domain
PF15410 - Pleckstrin homology domain

SCOP Domains:
101447 - Formin homology 2 domain (FH2 domain)
47576 - Calponin-homology domain, CH-domain
46966 - Spectrin repeat
50729 - PH domain-like
55060 - GHMP Kinase, C-terminal domain

ModBase Predicted Comparative 3D Structure on Q9H254
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003779 actin binding
GO:0005088 Ras guanyl-nucleotide exchange factor activity
GO:0005200 structural constituent of cytoskeleton
GO:0005515 protein binding
GO:0005543 phospholipid binding
GO:0019902 phosphatase binding
GO:0030506 ankyrin binding
GO:0030507 spectrin binding

Biological Process:
GO:0000165 MAPK cascade
GO:0002028 regulation of sodium ion transport
GO:0006888 ER to Golgi vesicle-mediated transport
GO:0007016 cytoskeletal anchoring at plasma membrane
GO:0007409 axonogenesis
GO:0007411 axon guidance
GO:0007605 sensory perception of sound
GO:0007628 adult walking behavior
GO:0009566 fertilization
GO:0010459 negative regulation of heart rate
GO:0016192 vesicle-mediated transport
GO:0019226 transmission of nerve impulse
GO:0021952 central nervous system projection neuron axonogenesis
GO:0022414 reproductive process
GO:0030534 adult behavior
GO:0033135 regulation of peptidyl-serine phosphorylation
GO:0034613 cellular protein localization
GO:0040018 positive regulation of multicellular organism growth
GO:0045162 clustering of voltage-gated sodium channels
GO:0051693 actin filament capping
GO:0061337 cardiac conduction
GO:0072659 protein localization to plasma membrane

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0005912 adherens junction
GO:0005938 cell cortex
GO:0008091 spectrin
GO:0014704 intercalated disc
GO:0016020 membrane
GO:0016363 nuclear matrix
GO:0016605 PML body
GO:0030424 axon
GO:0033268 node of Ranvier
GO:0033270 paranode region of axon
GO:0043025 neuronal cell body
GO:0043194 axon initial segment
GO:0043203 axon hillock
GO:0070062 extracellular exosome
GO:0070852 cell body fiber


-  Descriptions from all associated GenBank mRNAs
  AF324064 - Homo sapiens beta spectrin IV mRNA, complete cds.
AF324063 - Homo sapiens non-erythrocytic beta-spectrin 4 (SPNB4) mRNA, complete cds.
AF082075 - Homo sapiens beta4sigma1 spectrin mRNA, complete cds.
AF311855 - Homo sapiens spectrin beta IV (SPTBN3) mRNA, complete cds, alternatively spliced.
AY004227 - Homo sapiens betaIV spectrin isoform sigma4 mRNA, complete cds, alternatively spliced.
AY004226 - Homo sapiens betaIV spectrin isoform sigma2 and betaIV spectrin isoform sigma3 bicistronic mRNA, complete cds, alternatively spliced.
AB046862 - Homo sapiens mRNA for KIAA1642 protein, partial cds.
JD107861 - Sequence 88885 from Patent EP1572962.
JD443490 - Sequence 424514 from Patent EP1572962.
JD218363 - Sequence 199387 from Patent EP1572962.
AF311856 - Homo sapiens spectrin beta IV (SPTBN3) mRNA, complete cds, alternatively spliced.
AK309418 - Homo sapiens cDNA, FLJ99459.
AK308547 - Homo sapiens cDNA, FLJ98588.
AL133093 - Homo sapiens mRNA; cDNA DKFZp434J0328 (from clone DKFZp434J0328); partial cds.
LT220019 - Homo sapiens microRNA stbn4-miR1-3p.
AK054915 - Homo sapiens cDNA FLJ30353 fis, clone BRACE2007663.
JD419935 - Sequence 400959 from Patent EP1572962.
JD498406 - Sequence 479430 from Patent EP1572962.
JD534530 - Sequence 515554 from Patent EP1572962.
JD078651 - Sequence 59675 from Patent EP1572962.
JD051029 - Sequence 32053 from Patent EP1572962.
JD131603 - Sequence 112627 from Patent EP1572962.
JD413928 - Sequence 394952 from Patent EP1572962.
JD145853 - Sequence 126877 from Patent EP1572962.
JD288452 - Sequence 269476 from Patent EP1572962.
JD321893 - Sequence 302917 from Patent EP1572962.
JD195714 - Sequence 176738 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9H254 (Reactome details) participates in the following event(s):

R-HSA-391868 Dephosphorylation of NCAM1 bound pFyn
R-NUL-420388 Dephosphorylation of NCAM1 bound pFyn
R-HSA-391865 Recruitment of FAK to NCAM1:Fyn in lipid rafts
R-HSA-391871 Autophosphorylation of NCAM1 bound Fyn
R-HSA-392751 L1 linked to actin cytoskeleton by ankyrin
R-HSA-6807875 ARFGAP, cargo, v-SNAREs and p24 proteins bind nascent COPI complex
R-NUL-420398 Autophosphorylation of NCAM1 bound Fyn
R-HSA-391866 Phosphorylation of FAK by Src kinase
R-HSA-392051 Recruitment of Grb2 to pFAK:NCAM1
R-HSA-392053 SOS binds Grb2 bound to pFAK:NCAM1
R-HSA-373739 Ankyrins link voltage-gated sodium and potassium channels to spectrin and L1
R-HSA-6807877 ARFGAPs stimulate ARF GTPase activity
R-HSA-6809003 ERGIC-to-Golgi vesicles bind dynein:dynactin
R-HSA-392054 NCAM1:pFAK:Grb2:Sos-mediated nucleotide exchange of Ras
R-HSA-6809006 Vesicle is tethered through binding GOLGA2:GORASP1, GOLGB1 and the COG complex
R-HSA-6809011 cis-Golgi t-SNAREs bind YKT6 on tethered vesicle
R-HSA-5672965 RAS GEFs promote RAS nucleotide exchange
R-HSA-375165 NCAM signaling for neurite out-growth
R-HSA-445095 Interaction between L1 and Ankyrins
R-HSA-6807878 COPI-mediated anterograde transport
R-HSA-422475 Axon guidance
R-HSA-373760 L1CAM interactions
R-HSA-199977 ER to Golgi Anterograde Transport
R-HSA-1266738 Developmental Biology
R-HSA-199991 Membrane Trafficking
R-HSA-948021 Transport to the Golgi and subsequent modification
R-HSA-5673001 RAF/MAP kinase cascade
R-HSA-5653656 Vesicle-mediated transport
R-HSA-446203 Asparagine N-linked glycosylation
R-HSA-5684996 MAPK1/MAPK3 signaling
R-HSA-597592 Post-translational protein modification
R-HSA-5683057 MAPK family signaling cascades
R-HSA-392499 Metabolism of proteins
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: E9PGQ5, ENST00000598249.1, ENST00000598249.2, ENST00000598249.3, ENST00000598249.4, ENST00000598249.5, KIAA1642, NM_020971, Q9H1K7, Q9H1K8, Q9H1K9, Q9H253, Q9H254, Q9H3G8, Q9HCD0, SPTBN3, SPTN4_HUMAN, uc327cxw.1, uc327cxw.2
UCSC ID: ENST00000598249.6_5
RefSeq Accession: NM_020971.3
Protein: Q9H254 (aka SPTN4_HUMAN or SPCQ_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SPTBN4:
sptbn4 (SPTBN4 Disorder)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.